October 12, 2012

Ann Gibbons on slower mutation rate

I have covered several studies on the slower mutation rate and its implications, including a couple of recent overviews by Hawks and Scally and Durbin. Ann Gibbons has come up with yet another take on the matter in Science. There is also a freely available podcast on the topic; you can read the transcript. A couple of quotes from this interview:

Eight new studies in the past three years, and an older study, have all calculated the mutation rate directly. This is sort of the result of new high-throughput genome sequencing methods that give you high-quality coverage of the entire genome. So we’re able to get the more precise rate, which we sort of said is about an average of 36 mutations in each newborn. That’s something like a chance of getting 1.2 mutations per nucleotide site per 100 million years, okay? So when you think about spreading 36 mutations over three billion nucleic acids or bases in your genome, it comes out to not very many mutations per generation. This is the average rate in modern humans per generation, and it can be converted into a rate per year. Now there’s a little debate about how you do that because you have to know exactly how long each generation is. But new studies done by Linda Vigilant and her team – a number of primatologists in Germany – have studied the actual generation times using DNA and observations in the field of chimpanzees and gorillas, and we know them in modern humans. What this comes out to is about half the rate that researchers have been using for the past 15 years. One study by David Reich at Harvard and his colleagues comes up with a slower rate, but it isn’t half the rate. And that raises some questions about whether the new genome methods are actually catching all the mutations. We’re sort of at the limits of their resolution. I think most geneticists think that the rate is definitely slower. There is still some debate about precisely how much slower. Is it half or a little bit less?

...

Yes. So if you apply the new mutation rate, you get a human-chimpanzee split of about 8.3 million to about 10.1 million years ago, instead of 4-7 million years ago. So that’s quite a bit older. And the earliest fossils of the human family only are about 6-7 million years, so there’s a problem there. The human-Neandertal split used to be 250,000 to 350,000 years ago. Now it’s about 400-600 thousand years ago. That fits with fossils that look like they’re ancestral to Neandertals that show up around 500,000 years ago in Europe. So that’s a little better fit. And finally, we date the out-of-Africa migration to earlier, that we have our modern human ancestors coming out of Africa 90,000-130,000 years ago instead of less than 60,000 years ago. That would mean some of the fossils that have been discounted as modern human ancestors – especially in North Africa and Arabia – might actually be ancestral to modern humans if that’s accurate. There will be some debate. I would say at this point anthropologists and paleogeneticists who use these dates are quite confused, and they’re taking a wait-and-see attitude to see what geneticists end up deciding about applying these dates back in time.

One good thing to come out of the coming upheaval, as anthropologists scramble to update their models, is that the appearance of modern symbolic behavior and art. during the Upper Paleolithic will finally be decoupled from the Out-of-Africa event.

This will help us understand both: the ancestors of non-Africans did not come forth fully formed, like Athena from Zeus's head, having spent millennia of perfecting their craft and honing their minds by perforating shells and scratching lines in some South African cave. Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food. At the same time, the UP/LSA revolution may not have been effected by a new and improved type of human bursting into the scene and replacing Neandertals and assorted dummies, but rather as a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.

Researchers have used the number of mutations in DNA like a molecular clock to date key events in human evolution. Now it seems that the molecular clock ticks more slowly than anyone had thought, and many dates may need to be adjusted. Over the past 3 years, researchers have used new methods to sequence whole human genomes, allowing them to measure directly, for the first time, the average rate at which new mutations arise in a newborn baby. Most of these studies conclude that the mutation rate in humans today is roughly half the rate that has been used in many evolutionary studies since 2000, which would make genetic estimates of dates older than previously believed. The question now is how much older?

12 comments:

Maju, from the blog “for what they were we are” has been postulating this exact same scenario for many years now, so it is not new to the amateur geno-community, however, Ann Gibbons is a journalist, and what we need is nothing short of a fully peer-reviewed paper characterizing a revised mutation rate, along with the implications on paleogenetics, that is afforded by the increase of full genome sequences within the past few years before you can even initiate speculations such as these:“Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food.”

Incidentally, according to you, humans were just simply zombies searching for food so long as they remained in Africa, but lo and behold, once they leave Africa they become harbingers of “a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.”

Really? what exactly is it that stepping into the geographical space known as Eurasia that makes you acquire this acumen for bringing on such a 'revolution' by realizing this 'genetic potential', is it perhaps something in the air? Or perhaps the zombies, after the realization that they were no longer in Africa, said to themselves, look boys, we are no longer Africans, so let's go ahead and start that revolution that we had always wanted to start, Africa is no longer holding us back now.....

what we need is nothing short of a fully peer-reviewed paper characterizing a revised mutation rate.

Not sure what you mean there; there are several.

Incidentally, according to you, humans were just simply zombies searching for food so long as they remained in Africa, but lo and behold, once they leave Africa they become harbingers of “a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.”

If Out-of-Africa happened 100 thousand years ago, then it certainly happened by people who were still behaved largely in a non-modern way.

This has nothing to do with "as soon as they left Africa". I have been quite clear in the past that it was the combination of ecological crisis c. 70ka, moving away from the Sahara-Arabia belt and encountering new environments, and encountering other archaic humans (in both Sub-Saharan Africa and Eurasia) may have all combined to present a "shock" to modern humans that may have accelerated their cultural, and perhaps biological evolution.

The basic "hardware" or "brain wiring" for the UP may have already been there long before it was expressed in material form.

All modern humans today behave like zombies looking for food during their early years, but are thankfully extracted from that state by belonging to a _culture_ where a package of behavioral adaptations has become entrenched.

Really? what exactly is it that stepping into the geographical space known as Eurasia that makes you acquire this acumen for bringing on such a 'revolution' by realizing this 'genetic potential', is it perhaps something in the air?

I am not quite sure what you are arguing against. I maintained the exact opposite, that early Eurasians were not some kind of superman that were able to colonize the world and replace everybody else the moment they stepped OoA c. 60ka, but rather that they were just "regular folk" of their time, who followed the food OoA pre-100ka, and that the subsequent colonization of both Eurasia and Sub-Saharan Africa needs to be uncoupled from the event that brought some modern humans from Africa to Asia.

Isn't it a little premature to assume that the mutation rate in humans is the same for all groups?

It has already been shown that the recombination loci are highly divergent between Eurasians and Sub-Saharan Africans. Is it not also possible that the mutation rate may be different?

All of the studies that I am aware of suggesting a new, slower mutation rate are based in Europeans with the exception of the Youruba trio, which is only a single data point. More studies need to be done in all human groups to verify that the mutation rate is indeed universal.

Langergraber et .al (2012) 's work, although pushing back the Human-Chimp split time, hasn't solved exactly how much slower the actual mutation rate is relative to the conventional one in a manner that is conclusive enough to be accepted as the new academic orthodoxy, in addition, we don't know how much slower or faster this average mutation rate would have been in different time periods of the past, at what periods it would have regressed to, undershot or overshot the mean, not to mention the fact that an acceptable congruency of this new average mutation rate (or alternatively the postulated Human-Chimp split time) with fossil records has yet to be even established.

I am not quite sure what you are arguing against. I maintained the exact opposite, that early Eurasians were not some kind of superman that were able to colonize the world and replace everybody else the moment they stepped OoA c. 60ka, but rather that they were just "regular folk" of their time, who followed the food OoA pre-100ka, and that the subsequent colonization of both Eurasia and Sub-Saharan Africa needs to be uncoupled from the event that brought some modern humans from Africa to Asia.

You stress a distinction between your hypothetical 100 KYA Africa exiting humans with your hypothetical 'Out of Arabia' population post 70 KYA, and that somehow the 'Out of Arabia' population were the 'super-men' and the out of Africa population were the 'zombies', that is what I am arguing against, since I disagree with a distinctive out of Arabia population that some how transformed the paleolithic world, we certainly don't have any evidence for this from modern human genomes, as the primary genetic split of humanity is between Africans and non-Africans, not Arabians and non-Arabians, all the remaining subsequent splits happened in spatially limited zones of the world and do not even include all of humanity but just certain 'zones', while the 'revolution' would have included those inhabiting the blombos caves to the ancestors of the people that crossed the bearing straits to populate the Americas.

You stress a distinction between your hypothetical 100 KYA Africa exiting humans with your hypothetical 'Out of Arabia' population post 70 KYA, and that somehow the 'Out of Arabia' population were the 'super-men' and the out of Africa population were the 'zombies'

Not really. The Out-of-Arabians were more like refugees from an ecological crisis. The fact that they became ultimately very successful does not mean that they were supermen, it is just what happened. Human populations often face adversity: sometimes it kills them off, sometimes it drives them to success. In the case of the Out-of-Arabians it was success, but there is no reason to attribute this to any particular competency that other humans (e.g., Neandertals or different African groups) lacked.

Also, not all Out-of-Arabians seem to have participated in the UP revolution of Eurasia. It appears that that later event (taking place ~20ky after Out-of-Arabia) was associated with Y-haplogroup F descendants.

we certainly don't have any evidence for this from modern human genomes, as the primary genetic split of humanity is between Africans and non-Africans, not Arabians and non-Arabians

Arabia has gone through two extreme periods of desertification since 70kya. There is certainly no reason to expect a group humans to have remained in the place where they expanded from.

Also, the primary difference is indeed between Africans and non-Africans. This is due to both the Out-of-Africa event that took place before 100kya and was unrelated to the UP expansion of humans ~50kya, as well as the absorption of different groups of archaic humans in Africa and Eurasia.

"One good thing to come out of the coming upheaval, as anthropologists scramble to update their models, is that the appearance of modern symbolic behavior and art. during the Upper Paleolithic will finally be decoupled from the Out-of-Africa event".

***But these things appeared after years of cultural development, and not because a super-smart mutation swept the species, as evidenced by the fact that e.g., scientists from all continents, separated from each other by tens of thousands of years of evolution, can all be competent mechanics and mathematicians.***

I just came across this comment on gnxp - was wondering about Ed Miller's paper hereon the evolution of aboriginal intelligence? It seems they have exceptional abilities for spatial memory (and according herethe part of the brain used in processing and interpreting visual information – was about 25 per cent larger in aborigines than in Caucasians). However, the overall size is smaller and they perform less well on other psychometric measures. Miller theorises that more of the mutations that led to high intelligence occurred on continents with large populations than on less populated continents.

Not really. The Out-of-Arabians were more like refugees from an ecological crisis. The fact that they became ultimately very successful does not mean that they were supermen, it is just what happened.

We don't even know if those 'people' (note that any skeletal evidence for them is lacking), that produced those stone tools found in Oman had a successful expansion from there, they could just as easily have died out, only to be replaced with a fresh wave of Africans with a distinctive mtDNA L3 signature that post-dates the Toba eruption and is present in every living non-African today. There is absolutely no other find of 'nubian' type tools found beyond Oman, if they were successful in their expansion, then where are those 'nubian' type tools beyond Oman? Any pre-40 KYA tools found outside of Arabia and/or Africa are too ambiguous to be confidently ascribed to modern humans.

We don't even know if those 'people' (note that any skeletal evidence for them is lacking)

There is no reason to put 'people' in quotes. Whatever their physical anthropology, they were certainly people. And, if you are trying to suggest that they were not modern humans, then you must also accept that their counterparts in NE Africa making identical tools were also not modern humans.

a fresh wave of Africans with a distinctive mtDNA L3 signature that post-dates the Toba eruption

L3 does not post-date the Toba eruption; its estimated date is precisely at the time of the Toba eruption, and it will have to become somewhat older once the mtDNA clock is recalibrated to take into account a likely older human-chimp genetic divergence.

There is absolutely no other find of 'nubian' type tools found beyond Oman, if they were successful in their expansion, then where are those 'nubian' type tools beyond Oman?

The Nubian in Arabia was just discovered like a couple of years ago. You are in a big hurry. And, these were not the only people who made it Out-of-Africa prior to 100ka, they were also the Jebel Faya people (earlier), as well as the Mt. Carmel modern humans who used Mousterian tools.

So, there are many candidates for the group of modern people who expanded Out of Arabia. And, the critical question is not where are the Nubian tools, but rather why there is absolutely no archaeological evidence of whatever kind for Out-of-Africa c. 60kya. Where are the African tools?

Nubian technology has been found in association with a modern human child within occupation Phase 3 at the site of Taramsa 1 in Egypt. Science would suggest they're modern. Unless, of course, one is willing to propose an entirely new species that occupied NE Africa 100,000 years ago?

Nubian technology has now been identified in central Arabia (article in press by Crassard and Hilbert) and seems to be spread across central and eastern Yemen as well. The Mudayyan Industry, published in Usik et al. 2012, falls sometime after the Nubian occupation of Dhofar and is clearly derived from Nubian Levallois technology. Moreover, this particular technology governed by bidirectional recurrent Levallois blank production is interpreted as the transition from Middle Palaeolithic Levallois to Upper Palaeolithic blade reduction as exemplified at Initial Upper Palaeolithic sites in the Levant such as Boker Tachtit and Ain Difla. Essentially, the Nubians in Arabia have provided the technological missing link for the MP-UP transition in the Levant.

So, Nubians entered Arabia sometime between 130 - 100 ka and appear to have subsequently expanded northward during the early MIS 3 wet phase that would have facilitated north-south demographic exchange throughout the Peninsula. As for the Out of Arabia expansion eastward, this is still anyone's guess. We can be sure it wasn't related to Nubian Complex toolmakers.

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